This could be one of the Xbox one bugs. I use an unmodded controller when gaming, and am constantly having mic issues with the xbox one. The best bet (after the controller update) is to plug the mic into the controller before you power on the xbox one. even then I still have issues sometimes. This could also be NAT related. but in settings there is a "detailed network diagnostics" that states my connection is 36 down, 13 upload, ping of 91, with zero packet loss, and my NAT is set to open, so there is nothing wrong with my connection.
Last night during deadrising, With my mic plugged in, I could hear my friend, but he could not hear me. If I unplug the mic to just use kinect, he could hear me, but I could no longer hear him through the kinect.
So do not rule out this being an Xbox issue.